Researchers from Humboldt Universität zu Berlin describe a protocol to perform fast and non-arbitrary quality control of single-cell RNA sequencing (scRNA-seq) raw data using scKB and COPILOT. scKB is a wrapper script of kallisto and bustools for accelerated alignment and transcript count matrix generation, which runs significantly faster than the popular tool Cell Ranger. COPILOT then offers non-arbitrary background noise removal by comparing distributions of low-quality and high-quality cells. Together, this protocol streamlines the processing workflow and provides an easy entry for new scRNA-seq users.
COPILOT – fast scRNA-seq raw data processing using scKB and non-arbitrary quality control
Hsu CW, Shahan R, Nolan TM, Benfey PN, Ohler U. (2022) Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT. STAR Protoc 3(4):101729. [article]